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Leung CWB, Wall J, Esashi F. From rest to repair: Safeguarding genomic integrity in quiescent cells. DNA Repair (Amst) 2024; 142:103752. [PMID: 39167890 DOI: 10.1016/j.dnarep.2024.103752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024]
Abstract
Quiescence is an important non-pathological state in which cells pause cell cycle progression temporarily, sometimes for decades, until they receive appropriate proliferative stimuli. Quiescent cells make up a significant proportion of the body, and maintaining genomic integrity during quiescence is crucial for tissue structure and function. While cells in quiescence are spared from DNA damage associated with DNA replication or mitosis, they are still exposed to various sources of endogenous DNA damage, including those induced by normal transcription and metabolism. As such, it is vital that cells retain their capacity to effectively repair lesions that may occur and return to the cell cycle without losing their cellular properties. Notably, while DNA repair pathways are often found to be downregulated in quiescent cells, emerging evidence suggests the presence of active or differentially regulated repair mechanisms. This review aims to provide a current understanding of DNA repair processes during quiescence in mammalian systems and sheds light on the potential pathological consequences of inefficient or inaccurate repair in quiescent cells.
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Affiliation(s)
| | - Jacob Wall
- Sir William Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, South Parks Road, Oxford, UK.
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2
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Kassab MA, Chen Y, Wang X, He B, Brown EJ, Yu X. RNA 2'-O-methylation promotes persistent R-loop formation and AID-mediated IgH class switch recombination. BMC Biol 2024; 22:151. [PMID: 38977974 PMCID: PMC11232215 DOI: 10.1186/s12915-024-01947-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND RNA-DNA hybrids or R-loops are associated with deleterious genomic instability and protective immunoglobulin class switch recombination (CSR). However, the underlying phenomenon regulating the two contrasting functions of R-loops is unknown. Notably, the underlying mechanism that protects R-loops from classic RNase H-mediated digestion thereby promoting persistence of CSR-associated R-loops during CSR remains elusive. RESULTS Here, we report that during CSR, R-loops formed at the immunoglobulin heavy (IgH) chain are modified by ribose 2'-O-methylation (2'-OMe). Moreover, we find that 2'-O-methyltransferase fibrillarin (FBL) interacts with activation-induced cytidine deaminase (AID) associated snoRNA aSNORD1C to facilitate the 2'-OMe. Moreover, deleting AID C-terminal tail impairs its association with aSNORD1C and FBL. Disrupting FBL, AID or aSNORD1C expression severely impairs 2'-OMe, R-loop stability and CSR. Surprisingly, FBL, AID's interaction partner and aSNORD1C promoted AID targeting to the IgH locus. CONCLUSION Taken together, our results suggest that 2'-OMe stabilizes IgH-associated R-loops to enable productive CSR. These results would shed light on AID-mediated CSR and explain the mechanism of R-loop-associated genomic instability.
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Affiliation(s)
- Muzaffer Ahmad Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA.
- Present address: Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yibin Chen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
- Present address: Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Xin Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
- Present address: Westlake University, Hangzhou, Zhejiang, P. R. China
| | - Bo He
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
- Present address: Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94705, USA
| | - Eric J Brown
- Present address: Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA.
- Present address: Westlake University, Hangzhou, Zhejiang, P. R. China.
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3
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Tambe A, MacCarthy T, Pavri R. Interpretable deep learning reveals the role of an E-box motif in suppressing somatic hypermutation of AGCT motifs within human immunoglobulin variable regions. Front Immunol 2024; 15:1407470. [PMID: 38863710 PMCID: PMC11165027 DOI: 10.3389/fimmu.2024.1407470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/13/2024] Open
Abstract
Introduction Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation induced deaminase (AID) is essential for robust, long-term humoral immunity against pathogen and vaccine antigens. AID mutates cytosines preferentially within WRCH motifs (where W=A or T, R=A or G and H=A, C or T). However, it has been consistently observed that the mutability of WRCH motifs varies substantially, with large variations in mutation frequency even between multiple occurrences of the same motif within a single V region. This has led to the notion that the immediate sequence context of WRCH motifs contributes to mutability. Recent studies have highlighted the potential role of local DNA sequence features in promoting mutagenesis of AGCT, a commonly mutated WRCH motif. Intriguingly, AGCT motifs closer to 5' ends of V regions, within the framework 1 (FW1) sub-region1, mutate less frequently, suggesting an SHM-suppressing sequence context. Methods Here, we systematically examined the basis of AGCT positional biases in human SHM datasets with DeepSHM, a machine-learning model designed to predict SHM patterns. This was combined with integrated gradients, an interpretability method, to interrogate the basis of DeepSHM predictions. Results DeepSHM predicted the observed positional differences in mutation frequencies at AGCT motifs with high accuracy. For the conserved, lowly mutating AGCT motifs in FW1, integrated gradients predicted a large negative contribution of 5'C and 3'G flanking residues, suggesting that a CAGCTG context in this location was suppressive for SHM. CAGCTG is the recognition motif for E-box transcription factors, including E2A, which has been implicated in SHM. Indeed, we found a strong, inverse relationship between E-box motif fidelity and mutation frequency. Moreover, E2A was found to associate with the V region locale in two human B cell lines. Finally, analysis of human SHM datasets revealed that naturally occurring mutations in the 3'G flanking residues, which effectively ablate the E-box motif, were associated with a significantly increased rate of AGCT mutation. Discussion Our results suggest an antagonistic relationship between mutation frequency and the binding of E-box factors like E2A at specific AGCT motif contexts and, therefore, highlight a new, suppressive mechanism regulating local SHM patterns in human V regions.
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Affiliation(s)
- Abhik Tambe
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
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4
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Lauring MC, Basu U. Somatic hypermutation mechanisms during lymphomagenesis and transformation. Curr Opin Genet Dev 2024; 85:102165. [PMID: 38428317 DOI: 10.1016/j.gde.2024.102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
B cells undergoing physiologically programmed or aberrant genomic alterations provide an opportune system to study the causes and consequences of genome mutagenesis. Activated B cells in germinal centers express activation-induced cytidine deaminase (AID) to accomplish physiological somatic hypermutation (SHM) of their antibody-encoding genes. In attempting to diversify their immunoglobulin (Ig) heavy- and light-chain genes, several B-cell clones successfully optimize their antigen-binding affinities. However, SHM can sometimes occur at non-Ig loci, causing genetic alternations that lay the foundation for lymphomagenesis, particularly diffuse large B-cell lymphoma. Thus, SHM acts as a double-edged sword, bestowing superb humoral immunity at the potential risk of initiating disease. We refer to off-target, non-Ig AID mutations - that are often but not always associated with disease - as aberrant SHM (aSHM). A key challenge in understanding SHM and aSHM is determining how AID targets and mutates specific DNA sequences in the Ig loci to generate antibody diversity and non-Ig genes to initiate lymphomagenesis. Herein, we discuss some current advances regarding the regulation of AID's DNA mutagenesis activity in B cells.
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Affiliation(s)
- Max C Lauring
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
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5
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Ando K, Nakamura Y, Kitao H, Shimokawa M, Kotani D, Bando H, Nishina T, Yamada T, Yuki S, Narita Y, Hara H, Ohta T, Esaki T, Hamamoto Y, Kato K, Yamamoto Y, Minashi K, Ohtsubo K, Izawa N, Kawakami H, Kato T, Satoh T, Okano N, Tsuji A, Yamazaki K, Yoshino T, Maehara Y, Oki E. Mutational spectrum of TP53 gene correlates with nivolumab treatment efficacy in advanced gastric cancer (TP53MUT study). Br J Cancer 2023; 129:1032-1039. [PMID: 37532830 PMCID: PMC10491760 DOI: 10.1038/s41416-023-02378-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/03/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Although nivolumab has a high efficacy, reliable biomarkers are needed to predict the efficacy. We evaluated the nivolumab efficacy according to the TP53 mutation in advanced gastric cancer patients enrolled in the GI-SCREEN project. METHODS Sequence data of tumour specimens and clinicopathological information of 913 patients with advanced gastric cancer who were enrolled between April 2015 and March 2017 were obtained from the GI-SCREEN database. The follow-up information of 266 patients treated with nivolumab was also provided. RESULTS Among 266 patients treated with nivolumab, the objective response rate (ORR) of TP53 wild type (wt) patients (24.6%) was higher than that of TP53 mutant patients (14.8%). Among TP53 mutant patients, the ORR of the frameshift type tended to be higher than the transition and transversion type (23.1%, 13.6%, and 13.0%, respectively). The median progression-free survival (PFS) was statistically longer in TP53 wt patients than in mutant patients (3.3 vs 2.1 months, HR 1.4, 95% CI 1.1-1.9). Among TP53 mutant patients, PFS was statistically longer in the frameshift type than in the transversion type. CONCLUSION Nivolumab showed better efficacy in TP53 wt patients than in mutant patients. Among TP53 mutant patients, the frameshift type may have efficacy from nivolumab treatment.
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Affiliation(s)
- Koji Ando
- Department of Surgery and Science, Kyushu University, Fukuoka, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
- Department for the Promotion of Drug and Diagnostic Development, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroyuki Kitao
- Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan
| | | | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Bando
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
- Department for the Promotion of Drug and Diagnostic Development, National Cancer Center Hospital East, Kashiwa, Japan
| | - Tomohiro Nishina
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama, Japan
| | - Takanobu Yamada
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Satoshi Yuki
- Department of Gastroenterology and Hepatology, Hokkaido University Hospital, Sapporo, Japan
| | - Yukiya Narita
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Hiroki Hara
- Department of Gastroenterology, Saitama Cancer Center, Kitaadachi-gun, Japan
| | - Takashi Ohta
- Department of Clinical Oncology, Kansai Rosai Hospital, Amagasaki, Japan
| | - Taito Esaki
- Department of Gastrointestinal and Medical Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Yasuo Hamamoto
- Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Ken Kato
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiyuki Yamamoto
- Department of Gastroenterology and Hepatology, University of Tsukuba Hospital, Tsukuba, Japan
| | - Keiko Minashi
- Division of Gastroenterology, Chiba Cancer Center, Chiba, Japan
| | - Koushiro Ohtsubo
- Division of Medical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Naoki Izawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hisato Kawakami
- Department of Medical Oncology, Kindai University Hospital, Osakasayama, Japan
| | - Takeshi Kato
- Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Taroh Satoh
- Center for Cancer Genomics and Precision Medicine, Osaka University Hospital, Suita, Japan
| | - Naohiro Okano
- Department of Medical Oncology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Akihito Tsuji
- Department of Clinical Oncology, Kagawa University Hospital, Kita-gun, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shunto-gun, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
- Department for the Promotion of Drug and Diagnostic Development, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yoshihiko Maehara
- Kyushu Central Hospital of the Mutual Aid Association of Public School Teachers, Fukuoka, Japan
| | - Eiji Oki
- Department of Surgery and Science, Kyushu University, Fukuoka, Japan.
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6
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Skrekas C, Limeta A, Siewers V, David F. Targeted In Vivo Mutagenesis in Yeast Using CRISPR/Cas9 and Hyperactive Cytidine and Adenine Deaminases. ACS Synth Biol 2023; 12:2278-2289. [PMID: 37486333 PMCID: PMC10443040 DOI: 10.1021/acssynbio.2c00690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Indexed: 07/25/2023]
Abstract
Directed evolution is a preferred strategy to improve the function of proteins such as enzymes that act as bottlenecks in metabolic pathways. Common directed evolution approaches rely on error-prone PCR-based libraries where the number of possible variants is usually limited by cellular transformation efficiencies. Targeted in vivo mutagenesis can advance directed evolution approaches and help to overcome limitations in library generation. In the current study, we aimed to develop a high-efficiency time-controllable targeted mutagenesis toolkit in the yeast Saccharomyces cerevisiae by employing the CRISPR/Cas9 technology. To that end, we fused the dCas9 protein with hyperactive variants of adenine and cytidine deaminases aiming to create an inducible CRISPR-based mutagenesis tool targeting a specific DNA sequence in vivo with extended editing windows and high mutagenesis efficiency. We also investigated the effect of guide RNA multiplexing on the mutagenesis efficiency both phenotypically and on the DNA level.
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Affiliation(s)
- Christos Skrekas
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
| | - Angelo Limeta
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
| | - Verena Siewers
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Florian David
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
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7
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AIDmut-Seq: a Three-Step Method for Detecting Protein-DNA Binding Specificity. Microbiol Spectr 2023; 11:e0378322. [PMID: 36533916 PMCID: PMC9927353 DOI: 10.1128/spectrum.03783-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transcriptional factors (TFs) and their regulons make up the gene regulatory networks. Here, we developed a method based on TF-directed activation-induced cytidine deaminase (AID) mutagenesis in combination with genome sequencing, called AIDmut-Seq, to detect TF targets on the genome. AIDmut-Seq involves only three simple steps, including the expression of the AID-TF fusion protein, whole-genome sequencing, and single nucleotide polymorphism (SNP) profiling, making it easy for junior and interdisciplinary researchers to use. Using AIDmut-Seq for the major quorum sensing regulator LasR in Pseudomonas aeruginosa, we confirmed that a few TF-guided C-T (or G-A) conversions occurred near their binding boxes on the genome, and a number of previously characterized and uncharacterized LasR-binding sites were detected. Further verification of AIDmut-Seq using various transcriptional regulators demonstrated its high efficiency for most transcriptional activators (FleQ, ErdR, GacA, ExsA). We confirmed the binding of LasR, FleQ, and ErdR to 100%, 50%, and 86% of their newly identified promoters by using in vitro protein-DNA binding assay. And real-time RT-PCR data validated the intracellular activity of these TFs to regulate the transcription of those newly found target promoters. However, AIDmut-Seq exhibited low efficiency for some small transcriptional repressors such as RsaL and AmrZ, with possible reasons involving fusion-induced TF dysfunction as well as low transcription rates of target promoters. Although there are false-positive and false-negative results in the AIDmut-Seq data, preliminary results have demonstrated the value of AIDmut-Seq to act as a complementary tool for existing methods. IMPORTANCE Protein-DNA interactions (PDI) play a central role in gene regulatory networks (GRNs). However, current techniques for studying genome-wide PDI usually involve complex experimental procedures, which prevent their broad use by scientific researchers. In this study, we provide a in vivo method called AIDmut-Seq. AIDmut-Seq involves only three simple steps that are easy to operate for researchers with basic skills in molecular biology. The efficiency of AIDmut-Seq was tested and confirmed using multiple transcription factors in Pseudomonas aeruginosa. Although there are still some defects regarding false-positive and false-negative results, AIDmut-Seq will be a good choice in the early stage of PDI study.
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8
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Zhao H, Hartono SR, de Vera KMF, Yu Z, Satchi K, Zhao T, Sciammas R, Sanz L, Chédin F, Barlow J. Senataxin and RNase H2 act redundantly to suppress genome instability during class switch recombination. eLife 2022; 11:e78917. [PMID: 36542058 PMCID: PMC9771370 DOI: 10.7554/elife.78917] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Class switch recombination generates distinct antibody isotypes critical to a robust adaptive immune system, and defects are associated with autoimmune disorders and lymphomagenesis. Transcription is required during class switch recombination to recruit the cytidine deaminase AID-an essential step for the formation of DNA double-strand breaks-and strongly induces the formation of R loops within the immunoglobulin heavy-chain locus. However, the impact of R loops on double-strand break formation and repair during class switch recombination remains unclear. Here, we report that cells lacking two enzymes involved in R loop removal-senataxin and RNase H2-exhibit increased R loop formation and genome instability at the immunoglobulin heavy-chain locus without impacting its transcriptional activity, AID recruitment, or class switch recombination efficiency. Senataxin and RNase H2-deficient cells also exhibit increased insertion mutations at switch junctions, a hallmark of alternative end joining. Importantly, these phenotypes were not observed in cells lacking senataxin or RNase H2B alone. We propose that senataxin acts redundantly with RNase H2 to mediate timely R loop removal, promoting efficient repair while suppressing AID-dependent genome instability and insertional mutagenesis.
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Affiliation(s)
- Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | | | - Zheyuan Yu
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
- Graduate Group in Biostatistics, University of California, DavisDavisUnited States
| | - Krishni Satchi
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Tracy Zhao
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California, DavisDavisUnited States
| | - Lionel Sanz
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Jacqueline Barlow
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
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9
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Heterologous expression of hAID in E. coli leads to the production of a splice isoform of AID: hAIDδC, a mystery to be explored. Protein Expr Purif 2022; 199:106149. [PMID: 35952962 DOI: 10.1016/j.pep.2022.106149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a key player that initiates antibody diversification in activated B-cell. AID mediates somatic hypermutation (SHM) and class switch recombination (CSR) via the deamination of cytosine to uracil at the Ig locus, resulting in the production of high-affinity antibodies. AID is predominantly restricted to Ig genes, whereas off-targeting of AID leads to lymphocyte-related malignancies. Interestingly, apart from FL-AID other splice isoforms of AID are highly expressed in the lymphocyte malignancies. In our study, we found that the heterologous expression of hAID-FL in E. coli cells produced two induced bands of hAID as demonstrated by SDS-PAGE and western blotting. Remarkably, peptide mapping data predicted that one band is hAID-FL and the other is its splice isoform, hAIDδE4a. To get an insight into why E. coli cells expressed hAID-FL and hAID variant, we mutated the 5' and 3' splice site of a putative intron of hAID, but it failed to produce only hAID-FL. Incidentally, hAID expressed with fusion partners also displayed two bands, and peptide mapping data strongly suggest that besides hAID-FL, the lower band showed a significant number of amino acids missing towards the C-terminal domain (named as hAIDδC). Our results are the first report to show that expression of recombinant hAID alone or irrespective of solubilization tags in E. coli cells produced hAID-FL and hAIDδC. It will be fascinating to explore the potential mechanism underlying the expression of hAIDδC from recombinant hAID plasmid in E. coli cells.
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10
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Peycheva M, Neumann T, Malzl D, Nazarova M, Schoeberl UE, Pavri R. DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations. Science 2022; 377:eabj5502. [DOI: 10.1126/science.abj5502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic
Myc
translocations during antibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome maintenance complexes alters replication origin activity, decreases translocations, and deregulates global RT. Ablating a single origin at
Myc
causes an early-to-late RT switch, loss of translocations, and reduced proximity with the immunoglobulin heavy chain (
Igh
) gene, its major translocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanism in translocation biogenesis linking DSB formation to DSB ligation.
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Affiliation(s)
- Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Ursula E. Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
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11
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Leung W, Teater M, Durmaz C, Meydan C, Chivu AG, Chadburn A, Rice EJ, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, Danko CG, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM. SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis. Cancer Discov 2022; 12:1782-1803. [PMID: 35443279 PMCID: PMC9262862 DOI: 10.1158/2159-8290.cd-21-1514] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/08/2022] [Accepted: 04/18/2022] [Indexed: 01/26/2023]
Abstract
SETD2 is the sole histone methyltransferase responsible for H3K36me3, with roles in splicing, transcription initiation, and DNA damage response. Homozygous disruption of SETD2 yields a tumor suppressor effect in various cancers. However, SETD2 mutation is typically heterozygous in diffuse large B-cell lymphomas. Here we show that heterozygous Setd2 deficiency results in germinal center (GC) hyperplasia and increased competitive fitness, with reduced DNA damage checkpoint activity and apoptosis, resulting in accelerated lymphomagenesis. Impaired DNA damage sensing in Setd2-haploinsufficient germinal center B (GCB) and lymphoma cells associated with increased AICDA-induced somatic hypermutation, complex structural variants, and increased translocations including those activating MYC. DNA damage was selectively increased on the nontemplate strand, and H3K36me3 loss was associated with greater RNAPII processivity and mutational burden, suggesting that SETD2-mediated H3K36me3 is required for proper sensing of cytosine deamination. Hence, Setd2 haploinsufficiency delineates a novel GCB context-specific oncogenic pathway involving defective epigenetic surveillance of AICDA-mediated effects on transcribed genes. SIGNIFICANCE Our findings define a B cell-specific oncogenic effect of SETD2 heterozygous mutation, which unleashes AICDA mutagenesis of nontemplate strand DNA in the GC reaction, resulting in lymphomas with heavy mutational burden. GC-derived lymphomas did not tolerate SETD2 homozygous deletion, pointing to a novel context-specific therapeutic vulnerability. This article is highlighted in the In This Issue feature, p. 1599.
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Affiliation(s)
- Wilfred Leung
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Biomedical Sciences, Cornell University, Ithaca, New York
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Ceyda Durmaz
- Graduate Program of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ashlesha Muley
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Jaison Arivalagan
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- New York Genome Center, New York, New York
- Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Sandeep S Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
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12
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Abstract
Activation-induced cytidine deaminase (AID) initiates somatic hypermutation of immunoglobulin (Ig) gene variable regions and class switch recombination (CSR) of Ig heavy chain constant regions. Two decades of intensive research has greatly expanded our knowledge of how AID functions in peripheral B cells to optimize antibody responses against infections, while maintaining tight regulation of AID to restrain its activity to protect B cell genomic integrity. The many exciting recent advances in the field include: 1) the first description of AID's molecular structure, 2) remarkable advances in high throughput approaches that precisely track AID targeting genome-wide, and 3) the discovery that the cohesion-mediate loop extrusion mechanism [initially discovered in V(D)J recombination studies] also governs AID-medicated CSR. These advances have significantly advanced our understanding of AID's biochemical properties in vitro and AID's function and regulation in vivo. This mini review will discuss these recent discoveries and outline the challenges and questions that remain to be addressed.
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13
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DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
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Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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14
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Liu MC, Fugmann SD. Measuring Mutator Enzyme Activity Using an E. coli-Based Colony Formation Assay. Methods Mol Biol 2022; 2421:103-114. [PMID: 34870814 DOI: 10.1007/978-1-0716-1944-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mutator enzymes alter the nucleotide sequences of DNA or RNA molecules; immune systems utilize them to destroy the integrity of pathogen genomes and to optimize immune mediators of the host. Their dysregulation has been linked to tumorigenesis in various tissues. Defining and comparing the activities of such mutator enzymes requires a robust versatile assay that is independent of their biological context as in vivo mutation rates are typically low. Here we provide detailed protocols for two widely used E. coli-based approaches that detect the activities of ectopically expressed cytidine deaminases on two distinct reporter genes: an extrachromosomal kanamycin-resistance gene or an endogenous chromosomal substrate, the rpoB gene-encoding RNA polymerase. The generation of mutations is in both cases measured in a colony formation assay. With appropriate modifications, these assays can be extended to study other mutator enzymes.
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Affiliation(s)
- Mei-Chen Liu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
- Center for Molecular and Clinical Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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15
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The role of HIRA-dependent H3.3 deposition and its modifications in the somatic hypermutation of immunoglobulin variable regions. Proc Natl Acad Sci U S A 2021; 118:2114743118. [PMID: 34873043 DOI: 10.1073/pnas.2114743118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The H3.3 histone variant and its chaperone HIRA are involved in active transcription, but their detailed roles in regulating somatic hypermutation (SHM) of immunoglobulin variable regions in human B cells are not yet fully understood. In this study, we show that the knockout (KO) of HIRA significantly decreased SHM and changed the mutation pattern of the variable region of the immunoglobulin heavy chain (IgH) in the human Ramos B cell line without changing the levels of activation-induced deaminase and other major proteins known to be involved in SHM. Except for H3K79me2/3 and Spt5, many factors related to active transcription, including H3.3, were substantively decreased in HIRA KO cells, and this was accompanied by decreased nascent transcription in the IgH locus. The abundance of ZMYND11 that specifically binds to H3.3K36me3 on the IgH locus was also reduced in the HIRA KO. Somewhat surprisingly, HIRA loss increased the chromatin accessibility of the IgH V region locus. Furthermore, stable expression of ectopic H3.3G34V and H3.3G34R mutants that inhibit both the trimethylation of H3.3K36 and the recruitment of ZMYND11 significantly reduced SHM in Ramos cells, while the H3.3K79M did not. Consistent with the HIRA KO, the H3.3G34V mutant also decreased the occupancy of various elongation factors and of ZMYND11 on the IgH variable and downstream switching regions. Our results reveal an unrecognized role of HIRA and the H3.3K36me3 modification in SHM and extend our knowledge of how transcription-associated chromatin structure and accessibility contribute to SHM in human B cells.
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16
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Brown AL, Collins CD, Thompson S, Coxon M, Mertz TM, Roberts SA. Single-stranded DNA binding proteins influence APOBEC3A substrate preference. Sci Rep 2021; 11:21008. [PMID: 34697369 PMCID: PMC8546098 DOI: 10.1038/s41598-021-00435-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
The cytidine deaminase, APOBEC3A (A3A), is a prominent source of mutations in multiple cancer types. These APOBEC-signature mutations are non-uniformly distributed across cancer genomes, associating with single-stranded (ss) DNA formed during DNA replication and hairpin-forming sequences. The biochemical and cellular factors that influence these specificities are unclear. We measured A3A's cytidine deaminase activity in vitro on substrates that model potential sources of ssDNA in the cell and found that A3A is more active on hairpins containing 4 nt ssDNA loops compared to hairpins with larger loops, bubble structures, replication fork mimics, ssDNA gaps, or linear DNA. Despite pre-bent ssDNAs being expected to fit better in the A3A active site, we determined A3A favors a 4 nt hairpin substrate only 2- to fivefold over linear ssDNA substrates. Addition of whole cell lysates or purified RPA to cytidine deaminase assays more severely reduced A3A activity on linear ssDNA (45 nt) compared to hairpin substrates. These results indicate that the large enrichment of A3A-driven mutations in hairpin-forming sequences in tumor genomes is likely driven in part by other proteins that preferentially bind longer ssDNA regions, which limit A3A's access. Furthermore, A3A activity is reduced at ssDNA associated with a stalled T7 RNA polymerase, suggesting that potential protein occlusion by RNA polymerase also limits A3A activity. These results help explain the small transcriptional strand bias for APOBEC mutation signatures in cancer genomes and the general targeting of hairpin-forming sequences in the lagging strand template during DNA replication.
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Affiliation(s)
- Amber L Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Christopher D Collins
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Secily Thompson
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Margo Coxon
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Tony M Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Steven A Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA.
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17
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Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.
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Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
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18
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Delgado-Benito V, Berruezo-Llacuna M, Altwasser R, Winkler W, Sundaravinayagam D, Balasubramanian S, Caganova M, Graf R, Rahjouei A, Henke MT, Driesner M, Keller L, Prigione A, Janz M, Akalin A, Di Virgilio M. PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification. J Exp Med 2021; 217:151913. [PMID: 32609329 PMCID: PMC7537392 DOI: 10.1084/jem.20200137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/20/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The establishment of protective humoral immunity is dependent on the ability of mature B cells to undergo antibody gene diversification while adjusting to the physiological stressors induced by activation with the antigen. Mature B cells diversify their antibody genes by class switch recombination (CSR) and somatic hypermutation (SHM), which are both dependent on efficient induction of activation-induced cytidine deaminase (AID). Here, we identified PDGFA-associated protein 1 (Pdap1) as an essential regulator of cellular homeostasis in mature B cells. Pdap1 deficiency leads to sustained expression of the integrated stress response (ISR) effector activating transcription factor 4 (Atf4) and induction of the ISR transcriptional program, increased cell death, and defective AID expression. As a consequence, loss of Pdap1 reduces germinal center B cell formation and impairs CSR and SHM. Thus, Pdap1 protects mature B cells against chronic ISR activation and ensures efficient antibody diversification by promoting their survival and optimal function.
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Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Berruezo-Llacuna
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robert Altwasser
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Wiebke Winkler
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marieta Caganova
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robin Graf
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ali Rahjouei
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marie-Thérèse Henke
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Madlen Driesner
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lisa Keller
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Alessandro Prigione
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Janz
- Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Berlin, Germany
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19
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Varlet E, Ovejero S, Martinez AM, Cavalli G, Moreaux J. Role of Polycomb Complexes in Normal and Malignant Plasma Cells. Int J Mol Sci 2020; 21:ijms21218047. [PMID: 33126754 PMCID: PMC7662980 DOI: 10.3390/ijms21218047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 02/01/2023] Open
Abstract
Plasma cells (PC) are the main effectors of adaptive immunity, responsible for producing antibodies to defend the body against pathogens. They are the result of a complex highly regulated cell differentiation process, taking place in several anatomical locations and involving unique genetic events. Pathologically, PC can undergo tumorigenesis and cause a group of diseases known as plasma cell dyscrasias, including multiple myeloma (MM). MM is a severe disease with poor prognosis that is characterized by the accumulation of malignant PC within the bone marrow, as well as high clinical and molecular heterogeneity. MM patients frequently develop resistance to treatment, leading to relapse. Polycomb group (PcG) proteins are epigenetic regulators involved in cell fate and carcinogenesis. The emerging roles of PcG in PC differentiation and myelomagenesis position them as potential therapeutic targets in MM. Here, we focus on the roles of PcG proteins in normal and malignant plasma cells, as well as their therapeutic implications.
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Affiliation(s)
- Emmanuel Varlet
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
| | - Sara Ovejero
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
- Department of Biological Hematology, CHU Montpellier, 34295 Montpellier, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
| | - Jerome Moreaux
- Institute of Human Genetics, UMR 9002 Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, 34396 Montpellier, France; (E.V.); (S.O.); (A.-M.M.); (G.C.)
- Department of Biological Hematology, CHU Montpellier, 34295 Montpellier, France
- UFR Medicine, University of Montpellier, 34003 Montpellier, France
- Institut Universitaire de France (IUF), 75005 Paris, France
- Correspondence: ; Tel.: +33-04-6733-7903
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20
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Sundaravinayagam D, Rahjouei A, Andreani M, Tupiņa D, Balasubramanian S, Saha T, Delgado-Benito V, Coralluzzo V, Daumke O, Di Virgilio M. 53BP1 Supports Immunoglobulin Class Switch Recombination Independently of Its DNA Double-Strand Break End Protection Function. Cell Rep 2020; 28:1389-1399.e6. [PMID: 31390554 PMCID: PMC6693562 DOI: 10.1016/j.celrep.2019.06.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/16/2019] [Accepted: 06/07/2019] [Indexed: 01/29/2023] Open
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector functions of antibodies. CSR occurs via the formation and non-homologous end joining (NHEJ) repair of programmed DNA double-strand breaks (DSBs) at the immunoglobulin heavy chain locus. The DNA repair factors 53BP1 and Rif1 promote NHEJ and CSR by protecting DSBs against resection. However, to what extent repression of DNA end resection contributes to CSR is unknown. Here, we show that B lymphocytes devoid of 53BP1-Rif1-dependent DSB end protection activity undergo robust CSR. Inactivation of specific sets of phospho-sites within 53BP1 N-terminal SQ/TQ motifs abrogates Rif1 recruitment and inhibition of resection but only mildly reduces CSR. Furthermore, mutations within 53BP1 oligomerization domain abolish CSR without substantially affecting DNA end processing. Thus, inhibition of DNA end resection does not correlate with CSR efficiency, indicating that regulation of DSB processing is not a key determinant step in CSR. 53BP1 oligomerization is largely dispensable for inhibition of DSB resection 53BP1 higher order oligomerization is a pre-requisite for CSR B lymphocytes devoid of 53BP1-Rif1 DSB end protection activity undergo robust CSR 53BP1-mediated DSB end mobility is dispensable for CSR
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Affiliation(s)
- Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Ali Rahjouei
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Dagnija Tupiņa
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Tannishtha Saha
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Violeta Coralluzzo
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Oliver Daumke
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
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21
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Tandon A, Birkenhagen J, Nagalla D, Kölker S, Sauer SW. ADP-dependent glucokinase as a novel onco-target for haematological malignancies. Sci Rep 2020; 10:13584. [PMID: 32788680 PMCID: PMC7423609 DOI: 10.1038/s41598-020-70014-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/06/2020] [Indexed: 11/22/2022] Open
Abstract
Warburg effect or aerobic glycolysis provides selective growth advantage to aggressive cancers. However, targeting oncogenic regulators of Warburg effect has always been challenging owing to the wide spectrum of roles of these molecules in multitude of cells. In this study, we present ADP-dependent glucokinase (ADPGK) as a novel glucose sensor and a potential onco-target in specifically high-proliferating cells in Burkitt’s lymphoma (BL). Previously, we had shown ADPGK to play a major role in T-cell activation and induction of Warburg effect. We now report ADPGK knock-out Ramos BL cells display abated in vitro and in vivo tumour aggressiveness, via tumour-macrophage co-culture, migration and Zebrafish xenograft studies. We observed perturbed glycolysis and visibly reduced markers of Warburg effect in ADPGK knock-out cells, finally leading to apoptosis. We found repression of MYC proto-oncogene, and up to four-fold reduction in accumulated mutations in translocated MYC in knock-out cells, signifying a successful targeting of the malignancy. Further, the activation induced differentiation capability of knock-out cells was impaired, owing to the inability to cope up with increased energy demands. The effects amplified greatly upon stimulation-based proliferation, thus providing a novel Burkitt’s lymphoma targeting mechanism originating from metabolic catastrophe induced in the cells by removal of ADPGK.
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Affiliation(s)
- Amol Tandon
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany. .,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
| | - Jana Birkenhagen
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Deepthi Nagalla
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Stefan Kölker
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Sven Wolfgang Sauer
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
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22
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Immunoglobulin Class Switch Recombination Is Initiated by Rare Cytosine Deamination Events at Switch Regions. Mol Cell Biol 2020; 40:MCB.00125-20. [PMID: 32513818 DOI: 10.1128/mcb.00125-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/01/2020] [Indexed: 11/20/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates immunoglobulin (Ig) class switch recombination (CSR), somatic hypermutation (SHM), and gene conversion by converting DNA cytosines to uracils at specific genomic regions. In this study, we examined AID footprints across the entire length of an engineered switch region in cells ablated for uracil repair. We found that AID deamination occurs predominantly at WRC hot spots (where W is A or T and R is A or G) and that the deamination frequency remains constant across the entire switch region. Importantly, we analyzed monoallelic AID deamination footprints on both DNA strands occurring within a single cell cycle. We found that AID generates few and mostly isolated uracils in the switch region, although processive AID deaminations are evident in some molecules. The frequency of molecules containing deamination on both DNA strands at the acceptor switch region correlates with the class switch efficiency, raising the possibility that the minimal requirement for DNA double-strand break (DSB) formation is as low as even one AID deamination event on both DNA strands.
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23
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Branton SA, Ghorbani A, Bolt BN, Fifield H, Berghuis LM, Larijani M. Activation-induced cytidine deaminase can target multiple topologies of double-stranded DNA in a transcription-independent manner. FASEB J 2020; 34:9245-9268. [PMID: 32437054 DOI: 10.1096/fj.201903036rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 12/30/2022]
Abstract
Activation-induced cytidine deaminase (AID) mutates immunoglobulin genes and acts genome-wide. AID targets robustly transcribed genes, and purified AID acts on single-stranded (ss) but not double-stranded (ds) DNA oligonucleotides. Thus, it is believed that transcription is the generator of ssDNA for AID. Previous cell-free studies examining the relationship between transcription and AID targeting have employed a bacterial colony count assay wherein AID reverts an antibiotic resistance stop codon in plasmid substrates, leading to colony formation. Here, we established a novel assay where kb-long dsDNA of varying topologies is incubated with AID, with or without transcription, followed by direct sequencing. This assay allows for an unselected and in-depth comparison of mutation frequency and pattern of AID targeting in the absence of transcription or across a range of transcription dynamics. We found that without transcription, AID targets breathing ssDNA in supercoiled and, to a lesser extent, in relaxed dsDNA. The most optimal transcription only modestly enhanced AID action on supercoiled dsDNA in a manner dependent on RNA polymerase speed. These data suggest that the correlation between transcription and AID targeting may reflect transcription leading to AID-accessible breathing ssDNA patches naturally occurring in de-chromatinized dsDNA, as much as being due to transcription directly generating ssDNA.
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Affiliation(s)
- Sarah A Branton
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Brittany N Bolt
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Heather Fifield
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Lesley M Berghuis
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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24
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Pham P, Malik S, Mak C, Calabrese PC, Roeder RG, Goodman MF. AID-RNA polymerase II transcription-dependent deamination of IgV DNA. Nucleic Acids Res 2020; 47:10815-10829. [PMID: 31566237 PMCID: PMC6846656 DOI: 10.1093/nar/gkz821] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022] Open
Abstract
Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) in immunoglobulin variable (IgV) genes to produce high-affinity antibodies. SHM requires IgV transcription by RNA polymerase II (Pol II). A eukaryotic transcription system including AID has not been reported previously. Here, we reconstitute AID-catalyzed deamination during Pol II transcription elongation in conjunction with DSIF transcription factor. C→T mutations occur at similar frequencies on non-transcribed strand (NTS) and transcribed strand (TS) DNA. In contrast, bacteriophage T7 Pol generates NTS mutations predominantly. AID-Pol II mutations are strongly favored in WRC and WGCW overlapping hot motifs (W = A or T, R = A or G) on both DNA strands. Single mutations occur on 70% of transcribed DNA clones. Mutations are correlated over a 15 nt distance in multiply mutated clones, suggesting that deaminations are catalyzed processively within a stalled or backtracked transcription bubble. Site-by-site comparisons for biochemical and human memory B-cell mutational spectra in an IGHV3-23*01 target show strongly favored deaminations occurring in the antigen-binding complementarity determining regions (CDR) compared to the framework regions (FW). By exhibiting consistency with B-cell SHM, our in vitro data suggest that biochemically defined reconstituted Pol II transcription systems can be used to investigate how, when and where AID is targeted.
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Affiliation(s)
- Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Chiho Mak
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter C Calabrese
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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25
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Ragu S, Matos-Rodrigues G, Lopez BS. Replication Stress, DNA Damage, Inflammatory Cytokines and Innate Immune Response. Genes (Basel) 2020; 11:E409. [PMID: 32283785 PMCID: PMC7230342 DOI: 10.3390/genes11040409] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/21/2022] Open
Abstract
Complete and accurate DNA replication is essential to genome stability maintenance during cellular division. However, cells are routinely challenged by endogenous as well as exogenous agents that threaten DNA stability. DNA breaks and the activation of the DNA damage response (DDR) arising from endogenous replication stress have been observed at pre- or early stages of oncogenesis and senescence. Proper detection and signalling of DNA damage are essential for the autonomous cellular response in which the DDR regulates cell cycle progression and controls the repair machinery. In addition to this autonomous cellular response, replicative stress changes the cellular microenvironment, activating the innate immune response that enables the organism to protect itself against the proliferation of damaged cells. Thereby, the recent descriptions of the mechanisms of the pro-inflammatory response activation after replication stress, DNA damage and DDR defects constitute important conceptual novelties. Here, we review the links of replication, DNA damage and DDR defects to innate immunity activation by pro-inflammatory paracrine effects, highlighting the implications for human syndromes and immunotherapies.
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Affiliation(s)
| | | | - Bernard S. Lopez
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, 24 rue du Faubourg St Jacques, 75014 Paris, France; (S.R.); (G.M.-R.)
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26
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Kazadi D, Lim J, Rothschild G, Grinstein V, Laffleur B, Becherel O, Lavin MJ, Basu U. Effects of senataxin and RNA exosome on B-cell chromosomal integrity. Heliyon 2020; 6:e03442. [PMID: 32195383 PMCID: PMC7075999 DOI: 10.1016/j.heliyon.2020.e03442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Loss of function of senataxin (SETX), a bona-fide RNA/DNA helicase, is associated with neuronal degeneration leading to Ataxia and Ocular Apraxia (AOA) in human patients. SETX is proposed to promote transcription termination, DNA replication, DNA repair, and to unwind deleterious RNA:DNA hybrids in the genome. In all the above-mentioned mechanisms, SETX unwinds transcription complex-associated nascent RNA which is then degraded by the RNA exosome complex. Here we have used B cells isolated from a SETX mutant mouse model and compared genomic instability and immunoglobulin heavy chain locus (IgH) class switch recombination (CSR) to evaluate aberrant and programmed genomic rearrangements, respectively. Similar to RNA exosome mutant primary B cells, SETX mutant primary B cells display genomic instability but a modest decrease in efficiency of CSR. Furthermore, knockdown of Setx mRNAs from CH12–F3 B-cell lines leads to a defect in IgA CSR and accumulation of aberrant patterns of mutations in IgH switch sequences. Given that SETX mutant mice do not recapitulate the AOA neurodegenerative phenotype, it is possible that some aspects of SETX biology are rescued by redundant helicases in mice. Overall, our study provides new insights into the role of the SETX/RNA exosome axis in suppressing genomic instability so that programmed DNA breaks are properly orchestrated.
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Affiliation(s)
- David Kazadi
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Veronika Grinstein
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Olivier Becherel
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Martin J Lavin
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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27
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Fan Y, Jiang W, Ran F, Luo R, An L, Hang H. An Efficient Exogenous Gene Insertion Site in CHO Cells with High Transcription Level to Enhance AID-Induced Mutation. Biotechnol J 2020; 15:e1900313. [PMID: 31975519 DOI: 10.1002/biot.201900313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/18/2019] [Indexed: 11/10/2022]
Abstract
Antibodies have been extensively used for the purpose of scientific research, clinical diagnosis, and therapy. Combination of in vitro somatic hypermutation and mammalian cell surface display has been an efficient technology for antibody or other proteins optimization, in which the efficiency of activation-induced cytidine deaminase (AID) mutations in genes is one of the most important key factors. Gene transcriptional level has been found to be positively proportional to AID-induced mutation frequency. Thus, construction of the cell clone bearing a gene of interest (GOI) with high transcription level can increase AID-induced mutations. In this study, a retargetable gene cassette is inserted onto predetermined chromosome site (ywhae gene site) which is among the genes with the highest as well as stable transcription, and is found that one subsite is suitable to be retargeted for efficient protein display in Chinese hamster ovary (CHO) cells. The resultant cell clone (T31) has higher and more stable transcription/expression than CHO-puro clone which was previously established through the strategy of random insertion followed by a high-throughput selection. It also possesses a significantly higher mutation frequency to GOI than CHO-puro cells; thus, it is a better clone for the in vitro improvement of antibody affinity, and probably other properties.
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Affiliation(s)
- Yingjun Fan
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Jiang
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fanlei Ran
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruiqi Luo
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili An
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiying Hang
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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28
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Hegazy YA, Fernando CM, Tran EJ. The balancing act of R-loop biology: The good, the bad, and the ugly. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49903-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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29
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Bobrovnitchaia I, Valieris R, Drummond RD, Lima JP, Freitas HC, Bartelli TF, de Amorim MG, Nunes DN, Dias-Neto E, da Silva IT. APOBEC-mediated DNA alterations: A possible new mechanism of carcinogenesis in EBV-positive gastric cancer. Int J Cancer 2020; 146:181-191. [PMID: 31090066 DOI: 10.1002/ijc.32411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/22/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2023]
Abstract
Mechanisms of viral oncogenesis are diverse and include the off-target activity of enzymes expressed by the infected cells, which evolved to target viral genomes for controlling their infection. Among these enzymes, the single-strand DNA editing capability of APOBECs represent a well-conserved viral infection response that can also cause untoward mutations in the host DNA. Here we show, after evaluating somatic single-nucleotide variations and transcriptome data in 240 gastric cancer samples, a positive correlation between APOBEC3s mRNA-expression and the APOBEC-mutation signature, both increased in EBV+ tumors. The correlation was reinforced by the observation of APOBEC mutations preferentially occurring in the genomic loci of the most active transcripts. This EBV infection and APOBEC3 mutation-signature axis were confirmed in a validation cohort of 112 gastric cancer patients. Our findings suggest that APOBEC3 upregulation in EBV+ cancer may boost the mutation load, providing further clues to the mechanisms of EBV-induced gastric carcinogenesis. After further validation, this EBV-APOBEC axis may prove to be a secondary driving force in the mutational evolution of EBV+ gastric tumors, whose consequences in terms of prognosis and treatment implications should be vetted.
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Affiliation(s)
- Irina Bobrovnitchaia
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Renan Valieris
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Rodrigo D Drummond
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Joao P Lima
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Medical Oncology Department, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | - Helano C Freitas
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
- Medical Oncology Department, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | - Thais F Bartelli
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | - Maria G de Amorim
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | - Diana N Nunes
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
- Laboratory of Neurosciences, Institute of Psychiatry, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Israel T da Silva
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
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30
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Hegazy YA, Fernando CM, Tran EJ. The balancing act of R-loop biology: The good, the bad, and the ugly. J Biol Chem 2019; 295:905-913. [PMID: 31843970 DOI: 10.1074/jbc.rev119.011353] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An R-loop is a three-stranded nucleic acid structure that consists of a DNA:RNA hybrid and a displaced strand of DNA. R-loops occur frequently in genomes and have significant physiological importance. They play vital roles in regulating gene expression, DNA replication, and DNA and histone modifications. Several studies have uncovered that R-loops contribute to fundamental biological processes in various organisms. Paradoxically, although they do play essential positive functions required for important biological processes, they can also contribute to DNA damage and genome instability. Recent evidence suggests that R-loops are involved in a number of human diseases, including neurological disorders, cancer, and autoimmune diseases. This review focuses on the molecular basis for R-loop-mediated gene regulation and genomic instability and briefly discusses methods for identifying R-loops in vivo It also highlights recent studies indicating the role of R-loops in DNA double-strand break repair with an updated view of much-needed future goals in R-loop biology.
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Affiliation(s)
- Youssef A Hegazy
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | | | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 .,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
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31
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Green AM, Weitzman MD. The spectrum of APOBEC3 activity: From anti-viral agents to anti-cancer opportunities. DNA Repair (Amst) 2019; 83:102700. [PMID: 31563041 PMCID: PMC6876854 DOI: 10.1016/j.dnarep.2019.102700] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
The APOBEC3 family of cytosine deaminases are part of the innate immune response to viral infection, but also have the capacity to damage cellular DNA. Detection of mutational signatures consistent with APOBEC3 activity, together with elevated APOBEC3 expression in cancer cells, has raised the possibility that these enzymes contribute to oncogenesis. Genome deamination by APOBEC3 enzymes also elicits DNA damage response signaling and presents therapeutic vulnerabilities for cancer cells. Here, we discuss implications of APOBEC3 activity in cancer and the potential to exploit their mutagenic activity for targeted cancer therapies.
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Affiliation(s)
- Abby M Green
- Division of Oncology, Children's Hospital of Philadelphia, United States; Division of Infectious Diseases, Children's Hospital of Philadelphia, United States; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, United States; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, United States; Department of Pediatrics, Washington University School of Medicine, United States.
| | - Matthew D Weitzman
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, United States; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, United States; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, United States.
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32
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Yu K, Lieber MR. Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 PMCID: PMC6856442 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
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Affiliation(s)
- Kefei Yu
- Michigan State University, Department of Microbiology & Molecular Genetics, 5175 Biomedical Physical Sciences, East Lansing, MI 48824
| | - Michael R. Lieber
- USC Norris Comprehensive Cancer Ctr., Departments of Pathology, of Molecular Microbiology & Immunology, of Biochemistry & Molecular Biology, and of the Section of Molecular & Computational Biology within the Department of Biological Sciences, 1441 Eastlake Ave., NTT5428, Los Angeles, CA 90089-9176
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33
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Distinct subtypes of diffuse large B-cell lymphoma defined by hypermutated genes. Leukemia 2019; 33:2662-2672. [PMID: 31186494 DOI: 10.1038/s41375-019-0509-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/26/2019] [Accepted: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a biologically and clinically heterogeneous disease whose personalized clinical management requires robust molecular stratification. Here, we show that somatic hypermutation (SHM) patterns constitute a marker for DLBCL molecular classification. The activity of SHM mutational processes delineated the cell of origin (COO) in DLBCL. Expression of the herein identified 36 SHM target genes stratified DLBCL into four novel SHM subtypes. In a meta-analysis of patients with DLBCL treated with immunochemotherapy, the SHM subtypes were significantly associated with overall survival (1642 patients) and progression-free survival (795 patients). Multivariate analysis of survival indicated that the prognostic impact of the SHM subtypes is independent from the COO classification and the International Prognostic Index. Furthermore, the SHM subtypes had a distinct clinical outcome within each of the COO subtypes, and strikingly, even within unclassified DLBCL. The genetic landscape of the four SHM subtypes indicated unique associations with driver alterations and oncogenic signaling in DLBCL, which suggests a possibility for therapeutic exploitation. These findings provide a biologically driven classification system in DLBCL with potential clinical applications.
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34
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Pilzecker B, Jacobs H. Mutating for Good: DNA Damage Responses During Somatic Hypermutation. Front Immunol 2019; 10:438. [PMID: 30915081 PMCID: PMC6423074 DOI: 10.3389/fimmu.2019.00438] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Somatic hypermutation (SHM) of immunoglobulin (Ig) genes plays a key role in antibody mediated immunity. SHM in B cells provides the molecular basis for affinity maturation of antibodies. In this way SHM is key in optimizing antibody dependent immune responses. SHM is initiated by targeting the Activation-Induced Cytidine Deaminase (AID) to rearranged V(D)J and switch regions of Ig genes. The mutation rate of this programmed mutagenesis is ~10-3 base pairs per generation, a million-fold higher than the non-AID targeted genome of B cells. AID is a processive enzyme that binds single-stranded DNA and deaminates cytosines in DNA. Cytosine deamination generates highly mutagenic deoxy-uracil (U) in the DNA of both strands of the Ig loci. Mutagenic processing of the U by the DNA damage response generates the entire spectrum of base substitutions characterizing SHM at and around the initial U lesion. Starting from the U as a primary lesion, currently five mutagenic DNA damage response pathways have been identified in generating a well-defined SHM spectrum of C/G transitions, C/G transversions, and A/T mutations around this initial lesion. These pathways include (1) replication opposite template U generates transitions at C/G, (2) UNG2-dependent translesion synthesis (TLS) generates transversions at C/G, (3) a hybrid pathway comprising non-canonical mismatch repair (ncMMR) and UNG2-dependent TLS generates transversions at C/G, (4) ncMMR generates mutations at A/T, and (5) UNG2- and PCNA Ubiquitination (PCNA-Ub)-dependent mutations at A/T. Furthermore, specific strand-biases of SHM spectra arise as a consequence of a biased AID targeting, ncMMR, and anti-mutagenic repriming. Here, we review mammalian SHM with special focus on the mutagenic DNA damage response pathways involved in processing AID induced Us, the origin of characteristic strand biases, and relevance of the cell cycle.
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Affiliation(s)
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
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35
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Activation-induced deaminase (AID) localizes to the nucleus in brief pulses. PLoS Genet 2019; 15:e1007968. [PMID: 30811383 PMCID: PMC6411215 DOI: 10.1371/journal.pgen.1007968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/11/2019] [Accepted: 01/16/2019] [Indexed: 11/19/2022] Open
Abstract
Activation-induced deaminase (AID) converts C to U and 5-methyl-C to T. These mutagenic activities are critical to immunoglobulin (Ig) gene diversification and epigenetic reprogramming, but they must be tightly controlled to prevent compromising cell fitness. AID acts in the nucleus but localizes predominately to the cytoplasm. To address this apparent paradox, we have carried out time-lapse imaging of AID in single living B cells and fibroblasts. We demonstrate that AID enters the nucleus in brief (30 min) pulses, evident in about 10% of cells in the course of a single cell cycle (24 hr imaging). Pulses do not depend on AID catalytic activity, but they are coordinated with nuclear accumulation of P53. Pulsing may protect cells from pathologic consequences of excess exposure to AID, or enable AID to synchronize its activity with transcription of genes that are AID targets or with nuclear entry of factors that act at sites of AID-catalyzed DNA deamination to promote Ig gene diversification or epigenetic reprogramming.
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36
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Abstract
Class switch recombination (CSR) generates isotype-switched antibodies with distinct effector functions essential for mediating effective humoral immunity. CSR is catalyzed by activation-induced deaminase (AID) that initiates DNA lesions in the evolutionarily conserved switch (S) regions at the immunoglobulin heavy chain (Igh) locus. AID-initiated DNA lesions are subsequently converted into DNA double stranded breaks (DSBs) in the S regions of Igh locus, repaired by non-homologous end-joining to effect CSR in mammalian B lymphocytes. While molecular mechanisms of CSR are well characterized, it remains less well understood how upstream signaling pathways regulate AID expression and CSR. B lymphocytes express multiple receptors including the B cell antigen receptor (BCR) and co-receptors (e.g., CD40). These receptors may share common signaling pathways or may use distinct signaling elements to regulate CSR. Here, we discuss how signals emanating from different receptors positively or negatively regulate AID expression and CSR.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
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37
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Briggs E, Crouch K, Lemgruber L, Lapsley C, McCulloch R. Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion. PLoS Genet 2018; 14:e1007729. [PMID: 30543624 PMCID: PMC6292569 DOI: 10.1371/journal.pgen.1007729] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/01/2018] [Indexed: 11/19/2022] Open
Abstract
Switching of the Variant Surface Glycoprotein (VSG) in Trypanosoma brucei provides a crucial host immune evasion strategy that is catalysed both by transcription and recombination reactions, each operating within specialised telomeric VSG expression sites (ES). VSG switching is likely triggered by events focused on the single actively transcribed ES, from a repertoire of around 15, but the nature of such events is unclear. Here we show that RNA-DNA hybrids, called R-loops, form preferentially within sequences termed the 70 bp repeats in the actively transcribed ES, but spread throughout the active and inactive ES, in the absence of RNase H1, which degrades R-loops. Loss of RNase H1 also leads to increased levels of VSG coat switching and replication-associated genome damage, some of which accumulates within the active ES. This work indicates VSG ES architecture elicits R-loop formation, and that these RNA-DNA hybrids connect T. brucei immune evasion by transcription and recombination.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Leandro Lemgruber
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
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38
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Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai JA, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon KR, Pękowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Di Virgilio M. The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination. Mol Cell 2018; 72:636-649.e8. [PMID: 30293785 PMCID: PMC6242708 DOI: 10.1016/j.molcel.2018.08.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/01/2018] [Accepted: 08/25/2018] [Indexed: 01/18/2023]
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector component of antibody responses. CSR is initiated by activation-induced cytidine deaminase (AID), which targets transcriptionally active immunoglobulin heavy chain (Igh) switch donor and acceptor DNA. The 3′ Igh super-enhancer, 3′ regulatory region (3′RR), is essential for acceptor region transcription, but how this function is regulated is unknown. Here, we identify the chromatin reader ZMYND8 as an essential regulator of the 3′RR. In B cells, ZMYND8 binds promoters and super-enhancers, including the Igh enhancers. ZMYND8 controls the 3′RR activity by modulating the enhancer transcriptional status. In its absence, there is increased 3′RR polymerase loading and decreased acceptor region transcription and CSR. In addition to CSR, ZMYND8 deficiency impairs somatic hypermutation (SHM) of Igh, which is also dependent on the 3′RR. Thus, ZMYND8 controls Igh diversification in mature B lymphocytes by regulating the activity of the 3′ Igh super-enhancer. ZMYND8 is required for GLT of acceptor S regions and Class Switch Recombination ZMYND8 supports efficient somatic hypermutation of the Igh variable regions ZMYND8 binds B cell super-enhancers, including the 3′ Igh enhancer ZMYND8 modulates the transcriptional status and activity of the 3′ Igh enhancer
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Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Daniel B Rosen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joy A Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Lisa Keller
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | | | | | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Madlen Driesner
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Roman I Subbotin
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
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39
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Moore CL, Papa LJ, Shoulders MD. A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo. J Am Chem Soc 2018; 140:11560-11564. [PMID: 29991261 PMCID: PMC6166643 DOI: 10.1021/jacs.8b04001] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Laboratory time scale evolution in vivo relies on the generation of large, mutationally diverse gene libraries to rapidly explore biomolecule sequence landscapes. Traditional global mutagenesis methods are problematic because they introduce many off-target mutations that are often lethal and can engender false positives. We report the development and application of the MutaT7 chimera, a potent and highly targeted in vivo mutagenesis agent. MutaT7 utilizes a DNA-damaging cytidine deaminase fused to a processive RNA polymerase to continuously direct mutations to specific, well-defined DNA regions of any relevant length. MutaT7 thus provides a mechanism for in vivo targeted mutagenesis across multi-kb DNA sequences. MutaT7 should prove useful in diverse organisms, opening the door to new types of in vivo evolution experiments.
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Affiliation(s)
- Christopher L Moore
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Louis J Papa
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Matthew D Shoulders
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
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40
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Song S, Matthias PD. The Transcriptional Regulation of Germinal Center Formation. Front Immunol 2018; 9:2026. [PMID: 30233601 PMCID: PMC6134015 DOI: 10.3389/fimmu.2018.02026] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022] Open
Abstract
Germinal centers (GCs) are essential structures of the humoral immune response, which form in the periphery in response to T cell dependent antigens. During the GC reaction, B cells undergo critical differentiation steps, which ultimately lead to the generation of antibodies with altered effector function and higher affinity for the selected antigen. Remarkably, many of the B cell tumors have their origin in the GCs; thus, understanding how the formation of these structures is regulated or deregulated is of high medical importance. This review gives an overview of the transcription factors that have been linked to the generation of GCs, and of their roles in the process.
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Affiliation(s)
- Shuang Song
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Patrick D Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
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41
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Liu MC, Liao WY, Buckley KM, Yang SY, Rast JP, Fugmann SD. AID/APOBEC-like cytidine deaminases are ancient innate immune mediators in invertebrates. Nat Commun 2018; 9:1948. [PMID: 29769532 PMCID: PMC5956068 DOI: 10.1038/s41467-018-04273-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/17/2018] [Indexed: 12/26/2022] Open
Abstract
In the course of both innate and adaptive immunity, cytidine deaminases within the activation induced cytidine deaminase (AID)/apolipoprotein B editing complex (APOBEC) family modulate immune responses by mutating specific nucleic acid sequences of hosts and pathogens. The evolutionary emergence of these mediators, however, seems to coincide precisely with the emergence of adaptive immunity in vertebrates. Here, we show a family of genes in species within two divergent invertebrate phyla-the echinoderm Strongylocentrotus purpuratus and the brachiopod Lingula anatina-that encode proteins with similarities in amino acid sequence and enzymatic activities to the vertebrate AID/APOBECs. The expression of these invertebrate factors is enriched in tissues undergoing constant, direct interactions with microbes and can be induced upon pathogen challenge. Our findings suggest that AID/APOBEC proteins, and their function in immunity, emerged far earlier than previously thought. Thus, cytidine deamination is probably an ancient innate immune mechanism that predates the protostome/deuterostome divergence.
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Affiliation(s)
- Mei-Chen Liu
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan
| | - Wen-Yun Liao
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan
| | - Katherine M Buckley
- Biological Sciences, Sunnybrook Research Institute, 2075 Bayview Ave., Toronto, ON, M4N 3M5, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, MG5 1LC, ON, Canada
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Shu Yuan Yang
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan
- Division of Biochemistry, Molecular and Cellular Biology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan District, Tao-Yuan, 333, Taiwan
- Department of Pathology, Chang Gung Memorial Hospital, Tao-Yuan, 333, Taiwan
| | - Jonathan P Rast
- Biological Sciences, Sunnybrook Research Institute, 2075 Bayview Ave., Toronto, ON, M4N 3M5, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, MG5 1LC, ON, Canada
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada
- Pathology & Laboratory Medicine, Emory University School of Medicine, 1462 Clifton Road, Atlanta, GA, 30322, USA
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan.
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan District, Tao-Yuan, 333, Taiwan.
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Kwei-Shan District, Tao-Yuan, 333, Taiwan.
- Department of General Surgery, Chang Gung Memorial Hospital, Tao-Yuan, 333, Taiwan.
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42
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Ribeiro de Almeida C, Dhir S, Dhir A, Moghaddam AE, Sattentau Q, Meinhart A, Proudfoot NJ. RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination. Mol Cell 2018; 70:650-662.e8. [PMID: 29731414 PMCID: PMC5971202 DOI: 10.1016/j.molcel.2018.04.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 03/02/2018] [Accepted: 03/30/2018] [Indexed: 12/20/2022]
Abstract
Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus.
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Affiliation(s)
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Ashish Dhir
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Amin E Moghaddam
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Quentin Sattentau
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK.
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43
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Yewdell WT, Chaudhuri J. A transcriptional serenAID: the role of noncoding RNAs in class switch recombination. Int Immunol 2018; 29:183-196. [PMID: 28535205 DOI: 10.1093/intimm/dxx027] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/22/2017] [Indexed: 12/31/2022] Open
Abstract
During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions and requires the DNA-modifying enzyme activation-induced cytidine deaminase (AID). AID-mediated DNA deamination within S regions initiates the formation of DNA double-strand breaks, which serve as biochemical beacons for downstream DNA repair pathways that coordinate the ligation of DNA breaks. Myriad factors contribute to optimal AID targeting; however, many of these factors also localize to genomic regions outside of the Igh locus. Thus, a current challenge is to explain the specific targeting of AID to the Igh locus. Recent studies have implicated noncoding RNAs in CSR, suggesting a provocative mechanism that incorporates Igh-specific factors to enable precise AID targeting. Here, we chronologically recount the rich history of noncoding RNAs functioning in CSR to provide a comprehensive context for recent and future discoveries. We present a model for the RNA-guided targeting of AID that attempts to integrate historical and recent findings, and highlight potential caveats. Lastly, we discuss testable hypotheses ripe for current experimentation, and explore promising ideas for future investigations.
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Affiliation(s)
- William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer, New York, NY 10065, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
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44
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Nicolas L, Cols M, Choi JE, Chaudhuri J, Vuong B. Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination. F1000Res 2018; 7:458. [PMID: 29744038 PMCID: PMC5904731 DOI: 10.12688/f1000research.13247.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2018] [Indexed: 01/03/2023] Open
Abstract
Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity.
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Affiliation(s)
- Laura Nicolas
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Montserrat Cols
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jee Eun Choi
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, NY, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bao Vuong
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, NY, USA
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45
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Castiblanco DP, Norton DD, Maul RW, Gearhart PJ. J H6 downstream intronic sequence is dispensable for RNA polymerase II accumulation and somatic hypermutation of the variable gene in Ramos cells. Mol Immunol 2018; 97:101-108. [PMID: 29625296 DOI: 10.1016/j.molimm.2018.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/09/2018] [Accepted: 03/30/2018] [Indexed: 02/03/2023]
Abstract
Activation-induced deaminase (AID) introduces nucleotide substitutions within the variable region of immunoglobulin genes to promote antibody diversity. This activity, which is limited to 1.5 kb downstream of the variable gene promoter, mutates both the coding exon and downstream intronic sequences. We recently reported that RNA polymerase II accumulates in these regions during transcription in mice. This build-up directly correlates with the area that is accessible to AID, and manipulation of RNA polymerase II levels alters the mutation frequency. To address whether the intronic DNA sequence by itself can regulate RNA polymerase II accumulation and promote mutagenesis, we deleted 613 bp of DNA downstream of the JH6 intron in the human Ramos B cell line. The loss of this sequence did not alter polymerase abundance or mutagenesis in the variable gene, suggesting that most of the intronic sequence is dispensable for somatic hypermutation.
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Affiliation(s)
- Diana P Castiblanco
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Darrell D Norton
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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46
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A licensing step links AID to transcription elongation for mutagenesis in B cells. Nat Commun 2018; 9:1248. [PMID: 29593215 PMCID: PMC5871760 DOI: 10.1038/s41467-018-03387-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 02/08/2018] [Indexed: 01/01/2023] Open
Abstract
Activation-induced deaminase (AID) mutates the immunoglobulin (Ig) genes to initiate somatic hypermutation (SHM) and class switch recombination (CSR) in B cells, thus underpinning antibody responses. AID mutates a few hundred other loci, but most AID-occupied genes are spared. The mechanisms underlying productive deamination versus non-productive AID targeting are unclear. Here we show that three clustered arginine residues define a functional AID domain required for SHM, CSR, and off-target activity in B cells without affecting AID deaminase activity or Escherichia coli mutagenesis. Both wt AID and mutants with single amino acid replacements in this domain broadly associate with Spt5 and chromatin and occupy the promoter of AID target genes. However, mutant AID fails to occupy the corresponding gene bodies and loses association with transcription elongation factors. Thus AID mutagenic activity is determined not by locus occupancy but by a licensing mechanism, which couples AID to transcription elongation. Activation-induced deaminase (AID) is important for inducing desirable mutations at the B cell receptor genes for effective antibody responses. Here the authors show that three key arginine residues of AID link AID-chromatin association with transcription elongation to license AID for specific mutagenesis in B cells.
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47
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DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner. Cell Rep 2017; 17:2927-2942. [PMID: 27974207 DOI: 10.1016/j.celrep.2016.11.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/07/2016] [Accepted: 11/11/2016] [Indexed: 11/22/2022] Open
Abstract
Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division.
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48
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Choudhary M, Tamrakar A, Singh AK, Jain M, Jaiswal A, Kodgire P. AID Biology: A pathological and clinical perspective. Int Rev Immunol 2017; 37:37-56. [PMID: 28933967 DOI: 10.1080/08830185.2017.1369980] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Activation-induced cytidine deaminase (AID), primarily expressed in activated mature B lymphocytes in germinal centers, is the key factor in adaptive immune response against foreign antigens. AID is responsible for producing high-affinity and high-specificity antibodies against an infectious agent, through the physiological DNA alteration processes of antibody genes by somatic hypermutation (SHM) and class-switch recombination (CSR) and functions by deaminating deoxycytidines (dC) to deoxyuridines (dU), thereby introducing point mutations and double-stranded chromosomal breaks (DSBs). The beneficial physiological role of AID in antibody diversification is outweighed by its detrimental role in the genesis of several chronic immune diseases, under non-physiological conditions. This review offers a comprehensive and better understanding of AID biology and its pathological aspects, as well as addresses the challenges involved in AID-related cancer therapeutics, based on various recent advances and evidence available in the literature till date. In this article, we discuss ways through which our interpretation of AID biology may reflect upon novel clinical insights, which could be successfully translated into designing clinical trials and improving patient prognosis and disease management.
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Affiliation(s)
- Meenal Choudhary
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Anubhav Tamrakar
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Amit Kumar Singh
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Monika Jain
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Ankit Jaiswal
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Prashant Kodgire
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
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Hoopes JI, Hughes AL, Hobson LA, Cortez LM, Brown AJ, Roberts SA. Avoidance of APOBEC3B-induced mutation by error-free lesion bypass. Nucleic Acids Res 2017; 45:5243-5254. [PMID: 28334887 PMCID: PMC5605239 DOI: 10.1093/nar/gkx169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/06/2017] [Indexed: 12/17/2022] Open
Abstract
APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR). However, strains without error-free lesion bypass proteins Ubc13, Mms2 and Mph1 displayed respective 4.9-, 2.8- and 7.8-fold higher frequency of APOBEC3B-induced CanR. These results indicate that mutations resulting from APOBEC activity are avoided by deoxyuridine conversion to abasic sites ahead of nascent lagging strand DNA synthesis and subsequent bypass by error-free template switching. We found this mechanism also functions during telomere re-synthesis, but with a diminished requirement for Ubc13. Interestingly, reduction of G to C substitutions in Ubc13-deficient strains uncovered a previously unknown role of Ubc13 in controlling the activity of the translesion synthesis polymerase, Rev1. Our results highlight a novel mechanism for error-free bypass of deoxyuridines generated within ssDNA and suggest that the APOBEC mutation signature observed in cancer genomes may under-represent the genomic damage these enzymes induce.
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Affiliation(s)
- James I Hoopes
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Amber L Hughes
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lauren A Hobson
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Luis M Cortez
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Alexander J Brown
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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Pavri R. R Loops in the Regulation of Antibody Gene Diversification. Genes (Basel) 2017; 8:E154. [PMID: 28574479 PMCID: PMC5485518 DOI: 10.3390/genes8060154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/24/2017] [Accepted: 05/31/2017] [Indexed: 01/06/2023] Open
Abstract
For nearly three decades, R loops have been closely linked with class switch recombination (CSR), the process that generates antibody isotypes and that occurs via a complex cascade initiated by transcription-coupled mutagenesis in switch recombination sequences. R loops form during transcription of switch recombination sequences in vitro and in vivo, and there is solid evidence that R loops are required for efficient class switching. The classical model of R loops posits that they boost mutation rates by generating stable and long tracts of single-stranded DNA that serve as the substrate for activation induced deaminase (AID), the enzyme that initiates the CSR reaction cascade by co-transcriptionally mutating ssDNA in switch recombination sequences. Though logical and compelling, this model has not been supported by in vivo evidence. Indeed, several reports suggest that R loops may not be involved in recruiting AID activity to switch regions, meaning that R loops probably serve other unanticipated roles in CSR. Here, I review the key findings in this field to date and propose hypotheses that could help towards elucidating the precise function of R loops in CSR.
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Affiliation(s)
- Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Campus Vienna Biocenter-1, Vienna Biocenter, Vienna 1030, Austria.
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